World of Microbiome

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.title[
# World of Microbiome
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.author[
### Ragavi Shanmugam • 28-Apr-2023
]
.institute[
### Zifo RnD Solutions
]

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## What is a Microbiome ?

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## What is Microbiome ?

* The microbiome is the community of microorganisms (such as fungi, bacteria and viruses) that 
exists in a particular environment (Types of Microbiome: 1. Soil Microbiome (Most complex) 2. 
Marine microbiome 3. Plant microbiome 4. Animal Microbiome (Ex. Chicken gut microbiome) 5. 
Human microbiome (Ex. Human gut microbiome)

* In humans, the term is often used to describe the microorganisms that live in or on a particular 
part of the body, such as the skin or gastrointestinal tract. These groups of microorganisms are 
dynamic and change in response to a host of environmental factors, such as exercise, diet, medication and other exposures.

* Microbiome research mostly looks at bacteria and fungi and rarely into archaea, viruses and other types.

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## Why study Microbiome ?

* We know the microbiome is important for maintaining human health, 
  and when things go wrong it can contribute to disease. In order to 
  understand how microbes, influence human disease, we first need to 
  understand the microbial make up of a healthy person—what types of 
  microbes are present, and what are they doing?

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## What is bacteria ?

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* Bacterial Genome:

1. Single chromosome 
  2. Mostly circular 
  3. Contains about 500-7500 
     genes 
  4. Genome size ranges from 
     400kbp – 13 million base pairs

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## Prokaryote Ribose and 16S rRNA

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## 16S rRNA sequence

The 16S rRNA gene is used for phylogenetic studies as it is 
highly conserved between different species of bacteria and 
archaea. Provides very good resolution till genus level and to 
some extent species level. There could be one or more copies 
of 16SrRNA in a bacterial genome.

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## Comparison metagenomics VS. 16S rRNA

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## Comparison metagenomics VS. 16S rRNA

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## 16s rRNA processing pipeline

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## Shotgun Metagenomics Pipeline

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## Suites of analysis tools

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## The taxonomic and functional compositions of a microbiome

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## The taxonomic and functional compositions of a microbiome

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## Diversity estimates are a central topic in microbiome data analysis

### Alpha, Beta and Gamma diversity

* The α-diversity is just the diversity of each site (local species pool). 
* The β-diversity represents the differences in species composition 
  among sites. 
* The γ-diversity is the diversity of the entire landscape (regional species 
  pool). 
* Shannon index α-diversity Test- Shannon index measures how evenly 
  the microbes are distributed in a sample. It answers the question "How 
  different?" How are the microbes balanced to each other? Do we have 
  species evenness (similar abundance level) or do some species 
  dominate others? 
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## Diversity estimates are a central topic in microbiome data analysis

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## The developing gut microbiome and major influencing environmental factors

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## Bibliography

* [Tools for Analysis of the Microbiome](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7598837/)

* [Best practices for analysing microbiomes](http://users.encs.concordia.ca/~gregb/home/PDF/best-practices-analysing-microbiomes-nat2018.pdf)

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# Thank you. Questions?

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Graphics from <img src="./assets/freepik.jpg" style="max-height:20px; vertical-align:middle;"> 
Created: 28-Apr-2023 • James Ashmore • <a href="https://www.zifornd.com/category/omics-bioinformatics">Bioinformatics</a> • <a href="https://www.zifornd.com">Zifo</a>

]